Avidin



3D Structure of Avidin

Avidin (Av) is a protein found in egg white which binds biotin (vitamin B7) with high affinity. This property makes it a powerful tool in various protein pull-down assays. Similar proteins are strepavidin (StrAv) from the bacterium Streptomyces avidinii, Rhizavidin (RhiAv) from Rhizobium etli, Xenavidin from frog, and the avidin-related proteins AVR2 and AVR4. The N-acetylglucosamine sugars are shown as space filling objects in the image on the left.

Avidin is one of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.

Avidin is a tetrameric protein what in different words means that if we could, we would see a protein with four regions that look identical one to the other. However, to isolate the four regions as a whole in order to show the protein three dimensional structure has been quite diffucult so far and we just can see the three dimensional structure for two of those four units.

The binding affinity of biotin for the avidin receptors is very hight or in other words, the strength of the interations between the biotin and the avidin receptors is so strong that washing the biotin-avidin complex is not enough to remove the ligand from its pocket. This is not even possible by adding more biotin molecules to the system avidin-biotin. Once a biotin has bound a pocket in the avidin, it is almost imposible to remove it in a biologica system!

 Each monomer is an eight-stranded antiparallel beta-barrel. Binding of biotin involves a highly stabilized network of polar and hydrophobic interactions.

The presence of additional hydrophobic and hydrophilic groups in the binding site of avidin may account for its higher affinity constant.

Unexpectedly, a residual N-acetylglucosamine moiety was detected in the deglycosylated avidin monomer. These sugars appear along with the biotin but outside of the biotin binding pockets.

About this Structure
2AVI is a 2 chains structure of sequences from Gallus gallus. Full crystallographic information is available from OCA.

3D structures of Avidin
Update June 2011

3fdc, 2jgs, 2c4i, 1vyo, 1rav, 1ave – cAv – chicken

2a5b, 2a5c, 2a8g – cAv+deoxyribose

1nqn, 2cam – cAv (mutant)

1ldo, 1ldq, 1lel, 1ij8, 1avd, 2avi – cAV + biotin derivative

Strepavidin
2bc3, 2iza, 2izb, 2izc, 2izd, 2ize, 2rta, 2rtb, 2rtc - StrAv - Streptomyces avidinii

1rxh – StrAv (mutant)+ biotinyl p-nitroaniline

1rxj, 1rxk, 1nqm, 1kff, 1kl4, 1luq, 1mm9, 1moy, 1n4j, 1n7y, 1n9y, 1nbx, 1swf, 1swu, 3mm0, 3pk2 - StrAv (mutant)

1kl3, 1kl5 - StrAv (mutant) + strep-tag II peptide

1rst, 1rsu - StrAv + strep-tag II peptide

1df8, 1mep, 1n43, 1n9m, 1ndj, 1swg - StrAv (mutant)+biotin

1nc9 - StrAv (mutant)+iminobiotin

2izl, 2rtl, 2rtm, 2rtn, 2rto, 2rtp, 2rtq, 2rtr - StrAv +iminobiotin

1mk5, 1swd, 1swe, 2f01, 2gh7 - StrAv core+biotin

1swa, 1swb, 1swc - StrAv core

1swh, 1swj, 1swl, 1swo, 1swq, 1sws, 2y3e - StrAv core (mutant)

1swk, 1swn, 1swp, 1swr, 1swt, 3mg5, 2y3f - StrAv core (mutant) + biotin

1stp, 2izf, 2izg, 2izh, 2izi, 2izj, 2rtd, 2rte, 2rtf, 2rtg - StrAv +biotin 1hqq, 1hxl – StrAv + MP-2 (mutant)

1hy2 - StrAv + MP-1

1hxz - StrAv + MP-2

1pts, 1sld, 1sle, 1slg, 1str, 1sts, 1vwa, 1vwb, 1vwc, 1vwd, 1vwe, 1vwf, 1vwg, 1vwh, 1vwi, 1vwj, 1vwk, 1vwl, 1vwm, 1vwn, 1vwo, 1vwp, 1vwq, 1vwr, 2g5l - StrAv + peptide

1slf - StrAv + SO4

1sre, 1srf, 1srg, 1srh, 1sri, 1srj - StrAv + benzoic acid ligands

1lcv, 1lcw, 1lcz, 1i9h – StrAv+biotin derivative

2izk, 2rth, 2rti, 2rtj, 2rtk – StrAV+glycouril

2qcb, 2wpu – StrAv+Ru ligand

Rhizavidin
3ew1 – RhiAv – Rhizobium etli

3ew2 – RhiAV+biotin

Xenavidin
2uz2, 2uyw – XenAv – frog

Tamavidin
2zsc – TanAv – Tamogitake mushroom

AVR2
1wbi – cAVR2

AVR4
2fhl – cAVR4+biotinyl p-nitroaniline

2of9, 2ofa, 1y53 - cAVR4 (mutant)

2fhn, 2of8 - cAVR4 (mutant)+biotinyl p-nitroaniline

1y52, 1y55 - cAVR4 (mutant)+biotin